Readme.txt - Summary of data in repository for:

Dataset for Dichroic Calcite Reveals the Pathway from Additive Binding to Occlusion

Repository author: David C. Green, ORCID:0000-0002-0578-2369, email: david.green@hh.se

Compiled 28th April 2021

File name and contents:

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SEM_Raw.zip - SEM micrographs in tif format of crystals produced under the conditions described. 

Crystals were analyzed by scanning electron microscopy (SEM) using an FEI NanoSEM Nova 450. Images were then reformatted in DrawPlus v7 for presentation.

The files are named and arrange according to the growth method and conditions under which they were grown
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Confocal_Raw.zip - Raw confocal data, .czi format usable in ImageJ/Fiji

Confocal laser fluorescence microscopy (CLFM) was conducted using a Zeiss LSM510 Upright Confocal Microscope on samples grown directly on clean glass substrates under oil immersion where required. Laser and imaging settings were controlled with Zeiss ZEN software, where conditions tailored for Congo red were used (excitation at 488 nm, low pass emission filter at 550 nm). Final images were then rendered in ImageJ/Fiji

Files named according to the type of reaction conditions used to produce the sample:
DM 5mM samples (CDM_5mM_CR_stack_001 to 004)
Overgrowth (Overgrowth_104up_1)
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Spectroscopy_Raw.zip - UV-Vis spectroscopy. Files can be opened in Excel (.xlsx) Origin (.opj). Contains raw and background deleted data sets.

Data was obtained using an Avantes or OceanOptics spectrometer, with the signal collected using a fibre optic attached to an optical microscope column. The spectra were in transmission mode, and recorded for every 5 degree rotation of a linear polariser, which was placed on the light source.

The files are named according to the reaction conditions under which the Calcite/Congo red samples were produced. 
OG = overgrowth
CDM = carbonate direct method
ADM = ammonia diffusion method
All data is then compiled in "compiled data 030719.opj"
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opticalMicroscopy_Raw.zip - Micrographs taken using an optical microscope equiped with a linear polariser. the images in .jpg format were obtained at 15 degree intervals of rotation with respect to the linear polariser.

The files are grouped according to the method and conditions by which the samples were produced. They are then named according to the number of degrees of rotation of the sample with respect to the polariser from the starting position (0). 
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AFM.zip - Processed AFM micrographs of calcite/Congo red surfaces saved as Tif, openable in any image display software

AFM images were recorded using a Bruker Multimode 8 with a NanoScope V controller.  Images were collected in contact mode using silicon nitride cantilevers with nominal spring constants of 0.35 N·m-1 (Bruker SNL-10). The images were then rendered using Bruker's AFM data analysis software package. 

The images are named according to the time at which they were taken. 
Orientation = image taken from the sample alignment microscope, showing the orientation of the calcite substrate
Then in order:
0_00059, Overgrowth calcite with a fresh layer of calcite, no Congo red added
0_00002, Immediately after Congo red reached the chamber, followed by
0_00006 and,
0_00022; 
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Modelling.zip - Calculated data obtained from models of Congo red on calcite surfaces. Obtained by Robert Darkins (UCL)

Please consult the individual readmes for more information
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